This option allows the mail delivery process to query the Apache server to determine the true sender of a message when the nobody user sends a message. This option requires an additional connection to the webserver for each message that is sent by the user account nobody (when suPHP and mod_ruid2 are both disabled).

I have disabled this since I am running suPHP.

So should I ignore the information from cPanel Security Advisor since I run suPHP?

OR

Is it safe to run the recommended information from cPanel Security Advisor Enable “Query Apache server status"?

If you run SuPHP, mail from PHP scripts will originate from that domains cPanel user instead of "nobody." Basically, that option is irrelevant if you're using SuPHP, and I'd recommend sticking with SuPHP anyway. The only time mail comes from 'nobody' to begin with is if you're not using SuPHP (i.e. using the DSO handler).

If you run SuPHP, mail from PHP scripts will originate from that domains cPanel user instead of "nobody." Basically, that option is irrelevant if you're using SuPHP, and I'd recommend sticking with SuPHP anyway. The only time mail comes from 'nobody' to begin with is if you're not using SuPHP (i.e. using the DSO handler).